CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 847

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
S	847	R847K		nonsyn	aGa	aAa	629	629	1	24101-24103
S	847	R847T		nonsyn	aGa	aCa	263	263	1	24101-24103
S	847	R847R		syn	agA	agG	169	155	0.91716	24101-24103
S	847	R847R		syn	Aga	Cga	169	13	0.0769231	24101-24103
S	847	R847R		syn	AgA	CgG	169	1	0.00591716	24101-24103
S	847	R847I		nonsyn	aGa	aTa	98	97	0.989796	24101-24103
S	847	R847I		nonsyn	aGA	aTC	98	1	0.0102041	24101-24103
S	847	R847del		del	AGA	---	88	88	1	24101-24103
S	847	R847S		nonsyn	agA	agT	21	13	0.619048	24101-24103
S	847	R847S		nonsyn	agA	agC	21	7	0.333333	24101-24103
S	847	R847S		nonsyn	AGa	TCa	21	1	0.047619	24101-24103
S	847	R847G		nonsyn	Aga	Gga	15	14	0.933333	24101-24103
S	847	R847G		nonsyn	AgA	GgG	15	1	0.0666667	24101-24103
S	847	R847del1		del	agA	ag-	5	4	0.8	24101-24103
S	847	R847del1		del	Aga	-ga	5	1	0.2	24101-24103
S	847	R847del2		del	aGA	a--	4	4	1	24101-24103
S	847	R847X		nonsyn	Aga	Tga	2	2	1	24101-24103
S	847	R847M		nonsyn	aGA	aTG	1	1	1	24101-24103
S	847	R847A		nonsyn	AGa	GCa	1	1	1	24101-24103

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
S	847	R847K	aGa	aAa	629	629	All	0.00012
S	847	R847T	aGa	aCa	263	263	All	0.00005
S	847	R847R	agA	agG	155	169	All	0.00003
S	847	R847R	Aga	Cga	13	169	All	0.000002
S	847	R847R	AgA	CgG	1	169	All	0
S	847	R847K	aGa	aAa	168	168	B.1.617.2	0.000633
S	847	R847K	aGa	aAa	164	164	B.1.1.363	0.982036
S	847	R847I	aGa	aTa	97	98	All	0.000019
S	847	R847I	aGA	aTC	1	98	All	0
S	847	R847del	AGA	---	88	88	All	0.000017
S	847	R847T	aGa	aCa	77	77	B.1.1.7	0.000069
S	847	R847K	aGa	aAa	72	72	AY.61	0.007544
S	847	R847K	aGa	aAa	52	52	B.1.1.7	0.000047
S	847	R847del	AGA	---	31	31	B.1.1.7	0.000028
S	847	R847K	aGa	aAa	27	27	B.1.160	0.000842
S	847	R847R	agA	agG	26	26	B.1.177	0.000342
S	847	R847T	aGa	aCa	25	25	AY.4	0.000039
S	847	R847K	aGa	aAa	24	24	AY.75.1	0.004327
S	847	R847I	aGa	aTa	22	22	B.1.1.7	0.00002
S	847	R847S	agA	agT	13	21	All	0.000002
S	847	R847S	agA	agC	7	21	All	0.000001
S	847	R847S	AGa	TCa	1	21	All	0
S	847	R847R	agA	agG	18	20	B.1.1.7	0.000016
S	847	R847R	Aga	Cga	2	20	B.1.1.7	0.000002
S	847	R847K	aGa	aAa	19	19	AY.103	0.000118
S	847	R847T	aGa	aCa	17	17	D.2	0.001276
S	847	R847G	Aga	Gga	14	15	All	0.000003
S	847	R847G	AgA	GgG	1	15	All	0
S	847	R847R	agA	agG	8	15	B.1	0.000073
S	847	R847R	Aga	Cga	7	15	B.1	0.000064
S	847	R847R	agA	agG	14	14	B.1.236	0.028747
S	847	R847R	agA	agG	12	13	AY.4	0.000019
S	847	R847R	Aga	Cga	1	13	AY.4	0.000002
S	847	R847S	agA	agT	11	12	B.1.1.7	0.00001
S	847	R847S	AGa	TCa	1	12	B.1.1.7	0.000001
S	847	R847I	aGa	aTa	11	11	AY.4	0.000017
S	847	R847K	aGa	aAa	11	11	B.1.1	0.0002
S	847	R847T	aGa	aCa	10	10	B.1.617.2	0.000038
S	847	R847R	agA	agG	9	10	B.1.617.2	0.000034
S	847	R847R	Aga	Cga	1	10	B.1.617.2	0.000004
S	847	R847T	aGa	aCa	8	8	AY.103	0.00005
S	847	R847K	aGa	aAa	8	8	AY.71	0.0038
S	847	R847K	aGa	aAa	7	7	A.28	0.018519
S	847	R847K	aGa	aAa	7	7	AY.20	0.000272
S	847	R847T	aGa	aCa	7	7	AY.25	0.000042
S	847	R847I	aGa	aTa	7	7	AY.3	0.00007
S	847	R847T	aGa	aCa	7	7	B.1	0.000064
S	847	R847T	aGa	aCa	7	7	B.1.2	0.000062
S	847	R847R	agA	agG	7	7	B.1.637	0.000512
S	847	R847I	aGa	aTa	6	7	D.2	0.00045
S	847	R847I	aGA	aTC	1	7	D.2	0.000075
S	847	R847K	aGa	aAa	6	6	AY.4	0.000009
S	847	R847K	aGa	aAa	6	6	B.1	0.000055
S	847	R847T	aGa	aCa	6	6	B.1.177	0.000079
S	847	R847del1	agA	ag-	4	5	All	0.000001
S	847	R847del1	Aga	-ga	1	5	All	0
S	847	R847T	aGa	aCa	5	5	AY.43	0.000022
S	847	R847K	aGa	aAa	5	5	AY.43	0.000022
S	847	R847T	aGa	aCa	5	5	AY.44	0.00003
S	847	R847I	aGa	aTa	5	5	B.1	0.000046
S	847	R847I	aGa	aTa	5	5	B.1.1	0.000091
S	847	R847del	AGA	---	5	5	B.1.177	0.000066
S	847	R847R	agA	agG	5	5	P.1	0.000079
S	847	R847del2	aGA	a--	4	4	All	0.000001
S	847	R847T	aGa	aCa	4	4	AY.102	0.000106
S	847	R847T	aGa	aCa	4	4	AY.29	0.000063
S	847	R847K	aGa	aAa	4	4	AY.34	0.000388
S	847	R847del	AGA	---	4	4	AY.4	0.000006
S	847	R847T	aGa	aCa	4	4	AY.42	0.000161
S	847	R847R	agA	agG	3	4	AY.43	0.000013
S	847	R847R	AgA	CgG	1	4	AY.43	0.000004
S	847	R847R	agA	agG	4	4	AY.47	0.000124
S	847	R847T	aGa	aCa	4	4	AY.6	0.000165
S	847	R847T	aGa	aCa	4	4	B.1.1	0.000073
S	847	R847T	aGa	aCa	4	4	B.1.1.519	0.000159
S	847	R847R	agA	agG	4	4	B.1.596	0.000349
S	847	R847K	aGa	aAa	3	3	AY.102	0.00008
S	847	R847R	agA	agG	2	3	AY.103	0.000012
S	847	R847R	Aga	Cga	1	3	AY.103	0.000006
S	847	R847K	aGa	aAa	3	3	AY.114	0.000693
S	847	R847K	aGa	aAa	3	3	AY.120	0.000112
S	847	R847R	agA	agG	3	3	AY.3	0.00003
S	847	R847T	aGa	aCa	3	3	AY.3	0.00003
S	847	R847del	AGA	---	3	3	AY.4.5	0.000322
S	847	R847del	AGA	---	3	3	AY.43	0.000013
S	847	R847I	aGa	aTa	3	3	AY.43	0.000013
S	847	R847R	agA	agG	3	3	AY.44	0.000018
S	847	R847R	agA	agG	3	3	B.1.1.486	0.004732
S	847	R847R	agA	agG	3	3	B.1.1.519	0.000119
S	847	R847G	Aga	Gga	3	3	B.1.1.7	0.000003
S	847	R847del2	aGA	a--	3	3	B.1.1.7	0.000003
S	847	R847del	AGA	---	3	3	B.1.177.54	0.001819
S	847	R847R	agA	agG	3	3	B.1.2	0.000026
S	847	R847K	aGa	aAa	3	3	B.1.2	0.000026
S	847	R847R	agA	agG	3	3	B.1.234	0.000396
S	847	R847R	agA	agG	3	3	B.1.319	0.009146
S	847	R847T	aGa	aCa	3	3	B.1.488	0.6
S	847	R847K	aGa	aAa	3	3	B.1.526	0.000071
S	847	R847I	aGa	aTa	3	3	B.1.617.2	0.000011
S	847	R847del	AGA	---	2	2		0.111111
S	847	R847X	Aga	Tga	2	2	All	0
S	847	R847R	agA	agG	2	2	AY.100	0.000092
S	847	R847I	aGa	aTa	2	2	AY.102	0.000053
S	847	R847R	agA	agG	2	2	AY.117	0.000169
S	847	R847K	aGa	aAa	2	2	AY.118	0.000125
S	847	R847T	aGa	aCa	2	2	AY.119	0.000071
S	847	R847K	aGa	aAa	2	2	AY.23	0.000139
S	847	R847K	aGa	aAa	2	2	AY.32	0.001065
S	847	R847K	aGa	aAa	2	2	AY.39.1	0.000079
S	847	R847G	Aga	Gga	2	2	AY.4	0.000003
S	847	R847I	aGa	aTa	2	2	AY.4.2	0.000043
S	847	R847G	Aga	Gga	2	2	AY.43	0.000009
S	847	R847I	aGa	aTa	2	2	AY.44	0.000012
S	847	R847del	AGA	---	2	2	AY.46.2	0.001271
S	847	R847T	aGa	aCa	2	2	AY.5	0.000041
S	847	R847T	aGa	aCa	2	2	AY.98	0.000158
S	847	R847del	AGA	---	2	2	B.1	0.000018
S	847	R847del	AGA	---	2	2	B.1.1	0.000036
S	847	R847K	aGa	aAa	2	2	B.1.1.148	0.017544
S	847	R847del	AGA	---	2	2	B.1.1.236	0.013793
S	847	R847S	agA	agC	2	2	B.1.1.25	0.001137
S	847	R847T	aGa	aCa	2	2	B.1.1.284	0.000215
S	847	R847T	aGa	aCa	2	2	B.1.1.331	0.023256
S	847	R847G	Aga	Gga	2	2	B.1.177	0.000026
S	847	R847K	aGa	aAa	2	2	B.1.177	0.000026
S	847	R847del	AGA	---	2	2	B.1.177.4	0.000422
S	847	R847T	aGa	aCa	2	2	B.1.177.55	0.004662
S	847	R847T	aGa	aCa	2	2	B.1.179	0.007519
S	847	R847I	aGa	aTa	2	2	B.1.351	0.000059
S	847	R847T	aGa	aCa	2	2	B.1.351	0.000059
S	847	R847I	aGa	aTa	2	2	B.1.427	0.000101
S	847	R847K	aGa	aAa	2	2	B.1.429	0.000047
S	847	R847T	aGa	aCa	2	2	B.1.526	0.000047
S	847	R847del	AGA	---	1	1	A	0.000387
S	847	R847S	agA	agC	1	1	A.1	0.000282
S	847	R847K	aGa	aAa	1	1	A.1	0.000282
S	847	R847T	aGa	aCa	1	1	A.23.1	0.000704
S	847	R847T	aGa	aCa	1	1	AD.2	0.000219
S	847	R847I	aGa	aTa	1	1	AD.2	0.000219
S	847	R847del	AGA	---	1	1	AH.3	0.003802
S	847	R847I	aGa	aTa	1	1	AL.1	0.012987
S	847	R847A	AGa	GCa	1	1	All	0
S	847	R847M	aGA	aTG	1	1	All	0
S	847	R847I	aGa	aTa	1	1	AM.4	0.003571
S	847	R847K	aGa	aAa	1	1	AY.10	0.00053
S	847	R847R	agA	agG	1	1	AY.102	0.000027
S	847	R847I	aGa	aTa	1	1	AY.103	0.000006
S	847	R847T	aGa	aCa	1	1	AY.106	0.000335
S	847	R847K	aGa	aAa	1	1	AY.110	0.000113
S	847	R847T	aGa	aCa	1	1	AY.110	0.000113
S	847	R847G	Aga	Gga	1	1	AY.117	0.000085
S	847	R847del	AGA	---	1	1	AY.117	0.000085
S	847	R847T	aGa	aCa	1	1	AY.118	0.000063
S	847	R847I	aGa	aTa	1	1	AY.119	0.000035
S	847	R847R	agA	agG	1	1	AY.119	0.000035
S	847	R847del	AGA	---	1	1	AY.120	0.000037
S	847	R847R	agA	agG	1	1	AY.20	0.000039
S	847	R847R	agA	agG	1	1	AY.23	0.00007
S	847	R847T	aGa	aCa	1	1	AY.23	0.00007
S	847	R847S	agA	agC	1	1	AY.25	0.000006
S	847	R847I	aGa	aTa	1	1	AY.25	0.000006
S	847	R847del	AGA	---	1	1	AY.25	0.000006
S	847	R847K	aGa	aAa	1	1	AY.25	0.000006
S	847	R847I	aGa	aTa	1	1	AY.26	0.000028
S	847	R847I	aGa	aTa	1	1	AY.29	0.000016
S	847	R847K	aGa	aAa	1	1	AY.29	0.000016
S	847	R847R	agA	agG	1	1	AY.29.1	0.000221
S	847	R847M	aGA	aTG	1	1	AY.3	0.00001
S	847	R847del	AGA	---	1	1	AY.3.1	0.000085
S	847	R847K	aGa	aAa	1	1	AY.33	0.000067
S	847	R847T	aGa	aCa	1	1	AY.33	0.000067
S	847	R847del	AGA	---	1	1	AY.36	0.000148
S	847	R847K	aGa	aAa	1	1	AY.39	0.000025
S	847	R847I	aGa	aTa	1	1	AY.39	0.000025
S	847	R847R	agA	agG	1	1	AY.39	0.000025
S	847	R847T	aGa	aCa	1	1	AY.39	0.000025
S	847	R847T	aGa	aCa	1	1	AY.39.1	0.00004
S	847	R847del2	aGA	a--	1	1	AY.4	0.000002
S	847	R847S	agA	agC	1	1	AY.4	0.000002
S	847	R847T	aGa	aCa	1	1	AY.4.2	0.000022
S	847	R847T	aGa	aCa	1	1	AY.4.2.1	0.000149
S	847	R847del1	Aga	-ga	1	1	AY.4.5	0.000107
S	847	R847T	aGa	aCa	1	1	AY.40	0.000964
S	847	R847K	aGa	aAa	1	1	AY.42	0.00004
S	847	R847I	aGa	aTa	1	1	AY.42	0.00004
S	847	R847X	Aga	Tga	1	1	AY.43	0.000004
S	847	R847del1	agA	ag-	1	1	AY.43	0.000004
S	847	R847I	aGa	aTa	1	1	AY.46	0.000104
S	847	R847T	aGa	aCa	1	1	AY.46.1	0.001027
S	847	R847K	aGa	aAa	1	1	AY.46.4	0.000165
S	847	R847T	aGa	aCa	1	1	AY.47	0.000031
S	847	R847I	aGa	aTa	1	1	AY.5	0.000021
S	847	R847del	AGA	---	1	1	AY.5	0.000021
S	847	R847K	aGa	aAa	1	1	AY.5.3	0.000337
S	847	R847T	aGa	aCa	1	1	AY.54	0.000095
S	847	R847G	Aga	Gga	1	1	AY.55	0.000917
S	847	R847K	aGa	aAa	1	1	AY.67	0.000464
S	847	R847I	aGa	aTa	1	1	AY.68	0.000274
S	847	R847T	aGa	aCa	1	1	AY.7.2	0.000559
S	847	R847del	AGA	---	1	1	AY.75	0.000056
S	847	R847T	aGa	aCa	1	1	AY.81	0.001992
S	847	R847S	agA	agT	1	1	AY.9	0.000068
S	847	R847K	aGa	aAa	1	1	AY.92	0.000287
S	847	R847I	aGa	aTa	1	1	AY.92	0.000287
S	847	R847T	aGa	aCa	1	1	AY.95	0.000761
S	847	R847R	agA	agG	1	1	AY.98.1	0.000048
S	847	R847del	AGA	---	1	1	AY.98.1	0.000048
S	847	R847I	aGa	aTa	1	1	AY.98.1	0.000048
S	847	R847del	AGA	---	1	1	AY.99.1	0.001553
S	847	R847R	agA	agG	1	1	AZ.2	0.000821
S	847	R847R	Aga	Cga	1	1	B	0.000128
S	847	R847G	Aga	Gga	1	1	B.1	0.000009
S	847	R847R	agA	agG	1	1	B.1.1	0.000018
S	847	R847T	aGa	aCa	1	1	B.1.1.1	0.000327
S	847	R847T	aGa	aCa	1	1	B.1.1.157	0.000913
S	847	R847del	AGA	---	1	1	B.1.1.159	0.004673
S	847	R847T	aGa	aCa	1	1	B.1.1.217	0.003636
S	847	R847T	aGa	aCa	1	1	B.1.1.222	0.000204
S	847	R847K	aGa	aAa	1	1	B.1.1.29	0.010309
S	847	R847R	agA	agG	1	1	B.1.1.304	0.002809
S	847	R847del	AGA	---	1	1	B.1.1.312	0.001912
S	847	R847K	aGa	aAa	1	1	B.1.1.316	0.000925
S	847	R847I	aGa	aTa	1	1	B.1.1.37	0.000193
S	847	R847R	agA	agG	1	1	B.1.1.63	0.000386
S	847	R847X	Aga	Tga	1	1	B.1.1.7	0.000001
S	847	R847A	AGa	GCa	1	1	B.1.1.7	0.000001
S	847	R847del1	agA	ag-	1	1	B.1.1.7	0.000001
S	847	R847K	aGa	aAa	1	1	B.1.131	0.008772
S	847	R847R	agA	agG	1	1	B.1.158	0.02381
S	847	R847R	agA	agG	1	1	B.1.160	0.000031
S	847	R847T	aGa	aCa	1	1	B.1.160.8	0.001289
S	847	R847S	agA	agC	1	1	B.1.177	0.000013
S	847	R847del	AGA	---	1	1	B.1.177.17	0.000821
S	847	R847del	AGA	---	1	1	B.1.177.18	0.00116
S	847	R847R	agA	agG	1	1	B.1.177.19	0.001431
S	847	R847T	aGa	aCa	1	1	B.1.177.4	0.000211
S	847	R847I	aGa	aTa	1	1	B.1.177.56	0.000668
S	847	R847del	AGA	---	1	1	B.1.177.58	0.001332
S	847	R847I	aGa	aTa	1	1	B.1.177.60	0.000218
S	847	R847del	AGA	---	1	1	B.1.177.60	0.000218
S	847	R847del	AGA	---	1	1	B.1.177.63	0.002703
S	847	R847I	aGa	aTa	1	1	B.1.177.65	0.000665
S	847	R847T	aGa	aCa	1	1	B.1.177.73	0.000566
S	847	R847T	aGa	aCa	1	1	B.1.177.86	0.000183
S	847	R847del1	agA	ag-	1	1	B.1.177.87	0.000728
S	847	R847del	AGA	---	1	1	B.1.179	0.003759
S	847	R847G	Aga	Gga	1	1	B.1.2	0.000009
S	847	R847I	aGa	aTa	1	1	B.1.2	0.000009
S	847	R847del	AGA	---	1	1	B.1.2	0.000009
S	847	R847K	aGa	aAa	1	1	B.1.221	0.000071
S	847	R847I	aGa	aTa	1	1	B.1.221	0.000071
S	847	R847G	AgA	GgG	1	1	B.1.221	0.000071
S	847	R847T	aGa	aCa	1	1	B.1.240	0.000216
S	847	R847T	aGa	aCa	1	1	B.1.243	0.00007
S	847	R847R	agA	agG	1	1	B.1.243	0.00007
S	847	R847del	AGA	---	1	1	B.1.258	0.000067
S	847	R847T	aGa	aCa	1	1	B.1.270	0.005618
S	847	R847T	aGa	aCa	1	1	B.1.311	0.000275
S	847	R847K	aGa	aAa	1	1	B.1.333	0.010526
S	847	R847I	aGa	aTa	1	1	B.1.340	0.004292
S	847	R847R	agA	agG	1	1	B.1.351	0.00003
S	847	R847T	aGa	aCa	1	1	B.1.36	0.000146
S	847	R847del	AGA	---	1	1	B.1.36.18	0.00042
S	847	R847K	aGa	aAa	1	1	B.1.36.18	0.00042
S	847	R847T	aGa	aCa	1	1	B.1.36.29	0.000517
S	847	R847I	aGa	aTa	1	1	B.1.36.31	0.001751
S	847	R847T	aGa	aCa	1	1	B.1.369	0.000285
S	847	R847T	aGa	aCa	1	1	B.1.395	0.007042
S	847	R847T	aGa	aCa	1	1	B.1.427	0.00005
S	847	R847T	aGa	aCa	1	1	B.1.429	0.000024
S	847	R847T	aGa	aCa	1	1	B.1.438.1	0.000107
S	847	R847I	aGa	aTa	1	1	B.1.526	0.000024
S	847	R847R	agA	agG	1	1	B.1.617.1	0.000129
S	847	R847T	aGa	aCa	1	1	B.1.617.1	0.000129
S	847	R847del	AGA	---	1	1	B.1.617.2	0.000004
S	847	R847del1	agA	ag-	1	1	B.1.617.2	0.000004
S	847	R847S	agA	agT	1	1	B.1.617.2	0.000004
S	847	R847R	agA	agG	1	1	B.1.621	0.000089
S	847	R847T	aGa	aCa	1	1	B.1.637	0.000073
S	847	R847K	aGa	aAa	1	1	C.37	0.000116
S	847	R847S	agA	agC	1	1	D.2	0.000075
S	847	R847K	aGa	aAa	1	1	D.2	0.000075
S	847	R847del	AGA	---	1	1	P.1.13	0.000898
S	847	R847I	aGa	aTa	1	1	P.1.14	0.000048
S	847	R847T	aGa	aCa	1	1	P.1.14	0.000048
S	847	R847G	Aga	Gga	1	1	P.1.14	0.000048
S	847	R847del	AGA	---	1	1	P.1.15	0.000232
S	847	R847T	aGa	aCa	1	1	Q.1	0.000126
S	847	R847del	AGA	---	1	1	Q.2	0.000613
S	847	R847del	AGA	---	1	1	U.3	0.003861

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.